Molecular microbiology

For the journal, see Molecular Microbiology (journal).

Molecular microbiology is the branch of microbiology devoted to the study of the molecular principles of the physiological processes involved in the life cycle of prokaryotic and eukaryotic microorganisms such as bacteria, viruses, unicellular algae, fungi, and protozoa. This includes gene expression and regulation, genetic transfer, the synthesis of macromolecules, sub-cellular organization, cell to cell communication, and molecular aspects of pathogenicity and virulence.

Molecular microbiology is primarily involved in the interactions between the various cell systems of microorganisms including the interrelationship of DNA, RNA and protein biosynthesis and the manner in which these interactions are regulated.

Bacteria

Mainly because of their relative simplicity, ease of manipulation and growth in vitro, and importance in medicine, bacteria were instrumental in the development of molecular biology. The complete genome sequence for a large number of bacterial species is now available. A list of sequenced prokaryotic genomes is available. Molecular microbiology techniques are currently being used in the development of new genetically engineered vaccines, in bioremediation,^[1] biotechnology, food microbiology,^[2] probiotic research,^[3] antibacterial development^[4] and environmental microbiology.^[5]

Many bacteria have become model organisms for molecular studies.

Molecular techniques have had a direct influence on the clinical practice of medical microbiology. In many cases where traditional phenotypic methods of microbial identification and typing are insufficient or time-consuming, molecular techniques can provide rapid and accurate data, potentially improving clinical outcomes. Specific examples include:

• 16s rRNA sequencing to provide bacterial identifications
• Pulsed Field Gel Electrophoresis for strain typing of epidemiologically related organisms.
• Direct detection of genes related to resistance mechanisms, such as mecA gene in Staphylococcus aureus

Gene expression and regulation

Bacteria have evolved abilities to regulate gene expression in response to signals in the intracellular and extracellular environment. Key to this are the diverse macromolecules (proteins or RNA) that sense change through direct interactions with chemical or physical stimuli.^[6]

Bacterial pathogenesis

New infectious diseases are emerging and bacteria-induced illnesses, such as tuberculosis, whooping cough and typhoid fever, are still a major cause of global mortality. In recent decades the development of molecular biology and genetic tools has led to extensive studies on the molecular and cellular aspects of the virulence properties of pathogenic bacteria.^[7]

Bacterial glycomics

Glycans play diverse roles in bacterial physiology. Progress in the study of bacterial glycomics is advancing rapidly due to improvements in analytical methodologies and the development of new and innovative approaches for glycan isolation, characterization and synthesis. Research in bacterial glycomics could lead to the development of novel drugs, bioactive glycans and glycoconjugate vaccines.^[8]

Viruses

Viruses are important pathogens of humans and animals.^[9] Their genomes are relatively small. For these reasons they were among the first organisms to be fully sequenced. The complete DNA sequence of the Epstein-Barr virus was completed in 1984.^[10][11] Bluetongue virus (BTV) has been in the forefront of molecular studies for last three decades and now represents one of the best understood viruses at the molecular and structural levels.^[12][13] Other viruses such as Papillomavirus,^[14] Coronavirus,^[15] Caliciviruses,^[16] Paramyxoviruses^[17] and Influenza virus^[18][19] have also been extensively studied at the molecular level.

Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and diverse entities in the biosphere. Bacteriophages, or "phage", have been fundamental in the development of the science of molecular biology and became "model organisms" for probing the basic chemistry of life.^[20] The first DNA-genome project to be completed was the phage Φ-X174 in 1977. Φ29 phage, a phage of Bacillus, is a paradigm for the study of several molecular mechanisms of general biological processes, including DNA replication and regulation of transcription.^[20][21]

Gene Therapy

Some viruses are used as vectors for gene therapy. Virus vectors have been developed that mediate stable genetic modification of treated cells by chromosomal integration of the transferred vector genomes. Gammaretroviral and lentiviral vectors, for example, can be utilized in clinical gene therapy aimed at the long-term correction of genetic defects, e.g., in stem and progenitor cells. Gammaretroviral and lentiviral vectors have so far been used in more than 300 clinical trials, addressing treatment options for various diseases.^[22][23]

RNAi and viruses

The new technology of RNAi is emerging as a powerful modality for battling some of the most notoriously challenging viral clinical targets. In particular, this technology is being developed as a new therapeutic tool for fighting specific viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV) and respiratory viruses.^[24]

Technology

Polymerase chain reaction^[25][26] (PCR) is used in microbiology to amplify (replicate many times) a single DNA sequence. If required, the sequence can also be altered in predetermined ways. Real-time PCR is used for the rapid detection of microorganisms and is currently employed in diagnostic clinical microbiology laboratories, environmental analysis, food microbiology, and many other fields.^[27] The closely related technique of quantitative PCR (qPCR) permits the quantitative measurement of DNA or RNA molecules.

Loop-mediated isothermal amplification (LAMP) is a relatively new DNA amplification technique that is simple, rugged and low cost. In LAMP, the target sequence is amplified at a constant temperature using either two or three sets of primers and a polymerase with high strand displacement activity. LAMP is used in organizations engaged in combating infectious diseases such as tuberculosis, malaria, and sleeping sickness in developing regions and has been proposed for the detection of waterborne pathogens.^[5]

Gel electrophoresis is used routinely in microbiology to separate DNA, RNA, or protein molecules using an electric field by virtue of their size, shape or electric charge.

Southern blotting, northern blotting, western blotting and Eastern blotting are molecular techniques for detecting the presence of microbial DNA sequences (Southern), RNA sequences (northern), protein molecules (western) or protein modifications (Eastern).

DNA microarrays are used in microbiology as the modern alternative to the "blotting" techniques. Microarrays permit the exploration of thousands of sequences at one time. This technique is used in molecular microbiology to detect the presence of pathogens in a sample (air, water, organ tissue, etc.). It is also used to determine the genetic differences between two microbial strains.^[28]

DNA sequencing and genomics have been used for many decades in molecular microbiology studies. Due to their relatively small size, virus and bacterial genomes were the first to be completely analysed by DNA sequencing. A huge range of sequence and genomic data is now available for a number of species and strains of microorganisms.

Lab-on-a-chip (LOC) devices integrate and scale down laboratory functions and processes to a miniaturized chip format. Many LOC devices are used in a wide array of biomedical and other analytical applications including rapid pathogen detection, clinical diagnosis, forensic science, electrophoresis, flow cytometry, blood chemistry analysis, protein and DNA analysis. LOC devices can be fabricated from many types of material including various polymers, glass, or silicon, or combinations of these materials. A broad variety of fabrication technologies are used for LOC device fabrication. LOC systems have several common features including microfluidics and sensing capabilities. Microfluidics deals with fluid flow in tiny channels using flow control devices (e.g. channels, pumps, mixers and valves). Sensing capabilities, usually optical or electrochemical sensors, can also be integrated into the chip.^[28][29]

RNA interference (RNAi) was discovered as a cellular gene regulation mechanism in 1998, but several RNAi-based applications for gene silencing have already made it into clinical trials. RNA interference (RNAi) technology has formed the basis of novel tools for biological research and drug discovery.^[24][30]

Nanotechnology, the engineering and art of manipulating matter at the nanoscale (1-100 nm), offers the potential of novel nanomaterials with applications in microbiology, in particular environmental microbiology.^[31]

See also

• Microbiology
• Environmental microbiology
• Food microbiology
• Biofilms
• Industrial microbiology

References

1. ^ Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2. 
2. ^ Fratamico PM and Bayles DO (editor). (2005). Foodborne Pathogens: Microbiology and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-00-4. 
3. ^ Mayo, B; van Sinderen, D (editor) (2010). Bifidobacteria: Genomics and Molecular Aspects. Caister Academic Press. ISBN 978-1-904455-68-4. 
4. ^ Miller, AA; Miller, PF (editor) (2011). Emerging Trends in Antibacterial Discovery: Answering the Call to Arms. Caister Academic Press. ISBN 978-1-904455-89-9. 
5. ^ ^{a b} Sen, K; Ashbolt, NK (editor) (2010). Environmental Microbiology: Current Technology and Water Applications. Caister Academic Press. ISBN 978-1-904455-70-7. 
6. ^ Spiro, S; Dixon, R (editor) (2010). Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition. Caister Academic Press. ISBN 978-1-904455-69-1. 
7. ^ Locht, C; Simonet, M (editor) (2012). Bacterial Pathogenesis: Molecular and Cellular Mechanisms. Caister Academic Press. ISBN 978-1-904455-91-2. 
8. ^ Reid, CW; Twine, SM; Reid, AN (editor) (2012). Bacterial Glycomics: Current Research, Technology and Applications. Caister Academic Press. ISBN 978-1-904455-95-0. 
9. ^ Mettenleiter TC and Sobrino F (editors). (2008). Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. 
10. ^ Baer et al. (1984). "DNA sequence and expression of the B95-8 Epstein—Barr virus genome". Nature 310 (5974): 207–211. doi:10.1038/310207a0. PMID 6087149. 
11. ^ Robertson ES (editor). (2005). Epstein-Barr Virus. Caister Academic Press. ISBN 978-1-904455-03-5. 
12. ^ Roy P (2008). "Molecular Dissection of Bluetongue Virus". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. 
13. ^ Roy P (2008). "Structure and Function of Bluetongue Virus and its Proteins". Segmented Double-stranded RNA Viruses: Structure and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-21-9. 
14. ^ Campo MS (editor). (2006). Papillomavirus Research: From Natural History To Vaccines and Beyond. Caister Academic Press. ISBN 978-1-904455-04-2. 
15. ^ Thiel V (editor). (2007). Coronaviruses: Molecular and Cellular Biology. Caister Academic Press. ISBN 978-1-904455-16-5. 
16. ^ Hansman, GS (editor) (2010). Caliciviruses: Molecular and Cellular Virology. Caister Academic Press. ISBN 978-1-904455-63-9. 
17. ^ Samal, SK (editor) (2011). The Biology of Paramyxoviruses. Caister Academic Press. ISBN 978-1-904455-85-1. 
18. ^ Kawaoka Y (editor). (2006). Influenza Virology: Current Topics. Caister Academic Press. ISBN 978-1-904455-06-6. 
19. ^ Wang, Q; Tao, YJ (editors) (2010). Influenza: Molecular Virology. Caister Academic Press. ISBN 978-1-904455-57-8. 
20. ^ ^{a b} Mc Grath S and van Sinderen D (editors). (2007). Bacteriophage: Genetics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-14-1. 
21. ^ Graumann P (editor). (2007). Bacillus: Cellular and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-12-7. 
22. ^ Kurth, R; Bannert, N (editors) (2010). Retroviruses: Molecular Biology, Genomics and Pathogenesis. Caister Academic Press. ISBN 978-1-904455-55-4. 
23. ^ Desport, M (editors) (2010). Lentiviruses and Macrophages: Molecular and Cellular Interactions. Caister Academic Press. ISBN 978-1-904455-60-8. 
24. ^ ^{a b} Martinez, MA (editor) (2010). RNA Interference and Viruses: Current Innovations and Future Trends. Caister Academic Press. ISBN 978-1-904455-56-1. 
25. ^ Logan J, Edwards K, Saunders N (editors) (2009). Real-Time PCR: Current Technology and Applications. Caister Academic Press. ISBN 978-1-904455-39-4. 
26. ^ Kennedy, S; Oswald, N (editor) (2011). PCR Troubleshooting and Optimization: The Essential Guide. Caister Academic Press. ISBN 978-1-904455-72-1. 
27. ^ Mackay IM (editor). (2007). Real-Time PCR in Microbiology: From Diagnosis to Characterization. Caister Academic Press. ISBN 978-1-904455-18-9. 
28. ^ ^{a b} Herold, KE; Rasooly, A (editor) (2009). Lab-on-a-Chip Technology: Biomolecular Separation and Analysis. Caister Academic Press. ISBN 978-1-904455-47-9. 
29. ^ Herold, KE; Rasooly, A (editor) (2009). Lab-on-a-Chip Technology: Fabrication and Microfluidics. Caister Academic Press. ISBN 978-1-904455-46-2. 
30. ^ Morris, KV (editor) (2008). RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Caister Academic Press. ISBN 978-1-904455-25-7. 
31. ^ Cloete, TE (editor) (2010). Nanotechnology in Water Treatment Applications. Caister Academic Press. ISBN 978-1-904455-66-0. 

External links

• Microbiology
• University of Washington Medicine | Molecular Microbiology Division
• John Innes Centre | Molecular Microbiology Department